MBD6

methyl-CpG binding domain protein 6, the group of Methyl-CpG binding domain containing

Basic information

Region (hg38): 12:57520709-57530148

Links

ENSG00000166987 ∙ NCBI:114785 ∙ OMIM:619458 ∙ HGNC:20445 ∙ Uniprot:Q96DN6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MBD6 gene.

• Inborn genetic diseases (49 variants)
• not provided (10 variants)
• MBD6-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MBD6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			50	3	3	56
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	51	4	5

Variants in MBD6

This is a list of pathogenic ClinVar variants found in the MBD6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-57524385-T-A		not specified	Uncertain significance (Feb 06, 2023)
12-57524735-G-A			Likely benign (Feb 02, 2018)
12-57524969-C-T		not specified	Uncertain significance (Jun 30, 2022)
12-57524979-G-A			Benign (Apr 11, 2018)
12-57524987-C-T		not specified	Likely benign (May 09, 2022)
12-57524994-G-A		MBD6-related disorder	Likely benign (Jun 07, 2019)
12-57525064-A-G		not specified	Uncertain significance (Jul 16, 2021)
12-57525354-G-A		not specified	Uncertain significance (Dec 27, 2023)
12-57525437-C-A		not specified	Uncertain significance (Aug 15, 2023)
12-57525523-C-A		not specified	Uncertain significance (Dec 18, 2023)
12-57525620-C-T		not specified	Uncertain significance (Jun 09, 2022)
12-57525639-C-A			not provided (-)
12-57525731-C-G		not specified	Uncertain significance (Aug 05, 2023)
12-57525746-C-G			Benign (Mar 29, 2018)
12-57525774-C-T		not specified	Uncertain significance (Feb 14, 2023)
12-57525789-C-G		not specified	Uncertain significance (Dec 01, 2022)
12-57525800-C-T		not specified	Uncertain significance (May 01, 2022)
12-57525867-T-A		not specified	Uncertain significance (Jun 11, 2021)
12-57525870-T-A		not specified	Uncertain significance (Jun 11, 2021)
12-57525894-C-T		not specified	Uncertain significance (Jun 17, 2022)
12-57525918-C-T		not specified	Uncertain significance (May 04, 2022)
12-57525931-C-G		not specified	Uncertain significance (Dec 07, 2023)
12-57526005-C-T		not specified	Uncertain significance (Nov 18, 2022)
12-57526046-C-T		MBD6-related disorder	Benign (Dec 31, 2019)
12-57526077-C-T		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MBD6	protein_coding	protein_coding	ENST00000355673	11	9439

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000635	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.741	628	578	1.09	0.0000322	6190
Missense in Polyphen		66	48.63	1.3572		380
Synonymous	0.198	234	238	0.984	0.0000122	2466
Loss of Function	4.74	2	30.1	0.0665	0.00000172	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000189	0.000183
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000730	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to heterochromatin. Does not interact with either methylated or unmethylated DNA (in vitro).
• Pathway: Post-translational protein modification;Metabolism of proteins;UCH proteinases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.0550
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.82

Haploinsufficiency Scores

• pHI: 0.339
• hipred: N
• hipred_score: 0.456
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.803

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mbd6
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: mbd6
• Affected structure: definitive hemopoiesis
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: protein deubiquitination
• Cellular component: fibrillar center;nucleus;nucleoplasm;chromocenter
• Molecular function: DNA binding;chromatin binding